Remux?

[canaan]

So I recently had to recover an external HDD and I got back all of my MKV files.
However, when I play them now, I can't skip through the file because everytime I do that my media player try to buffer the file. I read somewhere that I can remux (rebuild?) the files which should correct the issue.

Can remuxing be done on a DS411j?

Edit: After doing some more reading, it sounds like Mkvtoolnix is what I need. Is this right?
Is mkvtoolnix/mkvmerge a GUI or command line?